Rwandan authorities welcomed the arrest, with Tharcisse Karugarama, Rwanda's justice minister, saying: "At long last the long arm of the law is finally taking its course."
Agathe Habyarimana has steadfastly denied involvement in the genocide.
The death of her husband, Juvenal Habyarimana, Rwanda's former president, in April 1994 when his aeroplane was shot down, marked the beginning of the Rwandan genocide.
In less than 100 days, 800,000 people were killed, most of them Tutsis, while most of those who perpetrated the violence were Hutus.
Agathe Habyarimana left Rwanda three days after her husband died and moved to France, but Rwandan authorities are convinced she played a key role in plotting the killings.
The head of Rwanda's genocide fugitive tracking unit said it had asked for Agathe Habyarimana's extradition.
"Our priority is to have her tried in Rwanda because this is where she committed crimes against the Rwandan people," Jean Bosco Mutangana said.
But a French foreign ministry spokesman said there had been no formal extradition request from Rwanda.
A French judicial source, who declined to be named, said it was unlikely that the French would send Agathe Habyarimana back home for trial.
Although Rwanda has abolished the death penalty, the central African country's prison system could well be viewed as incompatible with European standards, the source said.
France and Rwanda broke off diplomatic relations in 2006 after a Paris judge accused Paul Kagame, Rwanda's current president, and nine aides of shooting down Habyarimana's aircraft.
Sarkozy's visit to Rwanda last week was aimed at trying to improve diplomatic relations after years of acrimony.
Rwanda has accused the administration of Francois Mitterrand, the former French president, of having trained and armed the Hutu fighters who were behind the killings.
During his trip to Rwanda, Sarkozy stopped short of apologising for any French actions, but said Paris had failed to understand the situation.
"Errors of assessment and political mistakes were made here, and they led to absolutely tragic consequences," he said.